LAMMPS (8 Jul 2015)
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

read_data data.swm4-ndp
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 14
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude

fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
500 rigid bodies with 2000 atoms
  0.832099 = max distance from body owner to body atom
fix_modify RIGID temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
fix NVT DRUDES nvt temp 1 1 100.0
fix DTINV all drude/transform/inverse

thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 15.0906 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] 
       0            0    4568.0415    903.41148      3664.63    623.46454            0    2890.2449    157955.66   -157804.74    244591.08        13824    202.18534    295.64644    14.858785 
      20   0.60629702    3742.7991    5338.7966   -1595.9975    567.29055            0    662.23349    155098.48      -157924    31679.046    13979.575    1194.8336    1690.2267    201.65776 
      40    1.2431891    2752.9388    4407.9332   -1654.9944    792.86725            0    870.27523    154593.92   -157912.06    27392.302    14278.564     986.5045    1450.7624    56.079837 
      60     1.875339    1995.9775     3980.851   -1984.8735    660.64216            0    750.43214    154538.47   -157934.42    22242.676    14691.413    890.92262    1315.3403    40.305321 
      80     2.471236    1377.1261    3449.7879   -2072.6618    617.64243            0    605.75693    154628.63   -157924.69    17345.214    15201.397    772.06962    1146.6088     21.44718 
     100    3.0357449    886.38995    3038.4108   -2152.0208    537.89929            0    450.99962    154789.13   -157930.05    13299.227    15783.335    680.00257    1011.6773    15.016231 
     120     3.585844      488.055    2928.1336   -2440.0786    536.23164            0    334.88597    154620.05   -157931.25    8694.3472    16409.509     655.3223    977.40122    9.8538294 
     140     4.117424    160.14918    2538.5116   -2378.3624    509.19396            0    249.89205    154793.34   -157930.79    6363.1137    17053.486     568.1241    847.92526    7.2744139 
     160    4.6321139   -103.57595    2403.1613   -2506.7372    494.69822            0    144.07174    154790.83   -157936.34    4017.2005    17699.095    537.83243    803.44775    5.3901399 
     180     5.126441   -315.61252    2216.7944   -2532.4069    477.29447            0    80.852363    154842.41   -157932.96    1958.1627    18336.716    496.12314     741.4685     4.440167 
     200    5.6090059   -490.61276    2058.9074   -2549.5202    470.23217            0    80.799455    154831.63   -157932.18    1260.1943    18960.132    460.78771    688.92684    3.5878733 
     220    6.0495639   -644.09355    2001.1189   -2645.2125    494.11524            0    53.071997    154741.65   -157934.05   -16.373549    19564.819    447.85452    669.94663    2.7746068 
     240    6.5042329   -773.76581    1911.0759   -2684.8417    491.56501            0    36.579309    154722.88   -157935.86   -773.18555    20144.755    427.70271    639.97688    2.2989541 
     260    6.9512041     -886.818    1719.7038   -2606.5218    462.97731            0    47.595907    154814.45   -157931.55   -696.23419    20696.487    384.87324    575.96351    1.9229602 
     280    7.3921249   -983.57561    1659.2167   -2642.7923    476.06924            0    65.542713    154749.27   -157933.68   -1099.4208    21220.613     371.3361    555.78067    1.7042918 
     300    7.8054619   -1069.4015     1531.598   -2600.9995    487.38132            0    130.06616    154709.03   -157927.47   -548.86446    21717.521    342.77477    513.11788    1.4030219 
     320    8.2272029   -1144.9139     1562.933   -2707.8469    509.00464            0    127.16899    154591.31   -157935.33   -1516.7077    22190.692    349.78761    523.61225    1.4145866 
     340    8.6145689   -1216.4369    1511.7737   -2728.2106    518.42214            0    144.71934    154541.92   -157933.27    -1345.493    22636.556    338.33806    506.55234    1.2328234 
     360    9.0159991   -1279.8637    1435.4044   -2715.2681    525.01973            0    153.83119    154536.21   -157930.33    -1447.797    23056.471    321.24646     480.9789    1.1390786 
     380    9.4004741   -1340.2241    1391.5909    -2731.815    536.93555            0    180.52081    154483.31   -157932.58   -1315.0222    23450.141     311.4409    466.34776     1.004293 
     400    9.7971771   -1398.7544    1401.1636    -2799.918    547.12264            0    190.99461    154394.23   -157932.27   -1686.7786    23818.238     313.5833    469.59825   0.92621346 
     420    10.175245   -1450.5676    1355.0166   -2805.5842    555.43355            0    178.57277    154392.99   -157932.58   -1948.3006    24158.665     303.2555    454.12588   0.90821389 
     440    10.550016   -1501.2755    1336.6037   -2837.8792    573.29095            0    195.76657    154324.78   -157931.72    -1845.698    24470.004    299.13465    447.99648    0.8127319 
     460     10.93798   -1551.1246    1327.3311   -2878.4557    580.57019            0    206.92238    154267.88   -157933.83   -2059.7154    24752.911    297.05944    444.88976   0.80466605 
     480    11.304226   -1597.9166     1280.274   -2878.1906    596.27629            0     247.5201    154210.94   -157932.93   -1714.1239    25006.108    286.52794    429.10945   0.79188456 
     500     11.66949   -1645.4221    1303.9947   -2949.4168    620.22431            0    275.42964    154086.38   -157931.45   -1833.6239    25232.592    291.83668    437.06941   0.78754301 
     520    12.030775   -1692.7733    1261.2365   -2954.0098    639.32812            0    295.13753    154045.85   -157934.32   -1715.0443    25432.412    282.26732    422.73896   0.75950535 
     540    12.389967   -1739.3602    1247.1301   -2986.4903    666.88476            0    341.37591    153937.16   -157931.91   -1556.9492    25607.225    279.11027    418.00746   0.75767537 
     560    12.765452   -1783.4916    1212.3647   -2995.8563    669.09681            0      366.501    153899.16   -157930.62   -1543.0147    25758.368     271.3297    406.37068   0.70509124 
     580    13.122579   -1824.6061    1200.7205   -3025.3267    699.41498            0    409.47507    153794.95   -157929.16   -1053.8519    25887.592    268.72372    402.43012   0.77346975 
     600     13.47702   -1864.0982    1206.4231   -3070.5213     726.9912            0    439.25863     153695.5   -157932.27   -1130.6737      26000.4    269.99996    404.33899   0.78190692 
     620     13.82937   -1902.6883     1167.061   -3069.7493    741.54351            0    453.21801    153667.95   -157932.46   -921.61026    26097.341    261.19065    391.14672    0.7561126 
     640    14.180362   -1941.2814    1168.4808   -3109.7622     758.6291            0    484.81029    153578.39   -157931.59   -1084.6877    26180.233    261.50841    391.64626   0.70968727 
     660    14.527615   -1977.9114    1159.1979   -3137.1094    746.51288            0     452.2958    153598.59   -157934.51   -1424.6628     26247.07    259.43088    388.52145   0.73088365 
     680    14.875155   -2015.8231     1149.125   -3164.9481    730.41157            0    417.95266    153620.83   -157934.15   -1485.3138    26293.983    257.17653      385.144   0.72723522 
     700     15.22063   -2052.4439    1175.9011    -3228.345    735.43016            0    393.72125    153577.95   -157935.44   -1936.2883    26318.916    263.16908    394.10321   0.77446426 
     720    15.565813   -2092.4868    1137.4051    -3229.892    739.27374            0    431.22089    153537.92    -157938.3   -1669.6367     26318.64     254.5536    381.18868   0.77432854 
     740    15.926298   -2128.2671    1117.2535   -3245.5206    763.39303            0     451.2336    153475.75   -157935.89   -1554.5185    26294.984    250.04362    374.42691   0.77695221 
     760    16.273413   -2164.5578    1132.9117   -3297.4695    791.93983            0    493.17297    153351.43   -157934.01   -1464.3621    26250.086    253.54797    379.63211   0.87260304 
     780    16.620524   -2201.7367    1138.2941   -3340.0308    832.89022            0    542.69718    153217.14   -157932.76   -1185.0268    26186.538    254.75255    381.43046   0.88724559 
     800    16.968419   -2236.9734    1127.0464   -3364.0197    849.94855            0    579.03844    153137.36   -157930.36    -957.1991    26107.922    252.23529    377.65702    0.8873688 
     820    17.320858   -2274.0191    1152.6791   -3426.6982    878.53555            0    605.98285    153020.89    -157932.1   -1004.5494    26016.264    257.97196    386.24526   0.90940959 
     840    17.671788   -2312.5555    1157.6702   -3470.2257    915.53242            0    653.69994    152892.11   -157931.56   -793.45868    25912.528    259.08897    387.88866   0.97141875 
     860    18.021136   -2351.0088    1136.5124   -3487.5212    921.37408            0    665.09396    152857.19   -157931.18   -528.38134    25800.163    254.35382    380.78143   0.98986969 
     880    18.370286   -2387.3364    1155.2826    -3542.619    934.02359            0    660.06761    152795.05   -157931.76   -775.58796    25681.702    258.55463    386.99987    1.1470186 
     900    18.737898   -2425.9324    1151.5543   -3577.4867    936.00838            0    670.95003    152749.78   -157934.22   -883.49007    25555.357    257.72021    385.72656    1.1920669 
     920     19.09607    -2461.264     1119.906     -3581.17     931.8496            0     682.4928     152739.5   -157935.01   -890.93067    25420.635    250.63726    375.12148    1.1675653 
     940     19.45002   -2496.7293    1081.4763   -3578.2056    971.61744            0    731.21429    152653.33   -157934.36    -483.6151    25277.795    242.03662    362.20568    1.2144341 
     960    19.805087    -2527.097     1111.841    -3638.938     964.7058            0    704.68407    152623.89   -157932.22   -841.64397    25129.524     248.8323    372.33505    1.3291216 
     980    20.160533   -2560.1354    1096.9132   -3657.0486    954.19645            0    693.42648    152627.51   -157932.19    -949.1276    24974.275    245.49142     367.3853    1.2126954 
    1000    20.518917   -2592.9079    1053.7186   -3646.6266    959.23242            0    684.31399    152644.74   -157934.91   -869.15319    24811.035     235.8244    352.90011    1.2013298 
    1020    20.849072    -2623.091    1066.4493   -3689.5404    998.09604            0    709.32917     152535.4   -157932.37   -881.38225    24640.265    238.67355    357.17132    1.2006706 
    1040    21.194962    -2652.822     1083.618     -3736.44      1011.32            0    727.70427    152458.99   -157934.45    -815.2175    24461.841    242.51594    362.90994    1.2429114 
    1060    21.530151   -2683.6347    1074.3994   -3758.0341    1029.3659            0    763.93884     152381.4   -157932.73   -616.78933    24277.069    240.45279    359.82116     1.235143 
    1080    21.868091   -2715.2991    1094.3032   -3809.6022    1068.1764            0    785.28284    152272.57   -157935.63   -541.23611    24088.232     244.9073    366.48583    1.2604348 
    1100    22.209137   -2747.0371    1066.1644   -3813.2016    1080.2369            0    833.94072    152208.13   -157935.51   -217.98411    23897.246    238.60979     357.0619    1.2283546 
    1120    22.551618   -2774.9066    1084.3361   -3859.2427     1113.055            0    847.43384    152114.69   -157934.42   -77.787494    23707.475    242.67665    363.13214    1.2803322 
    1140    22.899431     -2803.21    1072.4113   -3875.6213    1090.9217            0    807.02034    152161.17   -157934.73   -668.47773    23520.606    240.00786    359.14316    1.2572349 
    1160    23.252016   -2834.8697    1052.5943    -3887.464    1096.5034            0    789.77107    152162.88   -157936.62   -589.78074    23331.777    235.57277    352.55512    1.1369148 
    1180    23.609597   -2863.7817    1031.8109   -3895.5926    1087.1932            0    789.79657    152165.44   -157938.03   -586.94333    23140.391    230.92139    345.60929    1.0837566 
    1200    23.970129   -2891.3631     1042.111   -3933.4741    1093.7082            0    775.83298     152136.1   -157939.12   -1109.7168    22947.229    233.22659    349.07035    1.0726257 
    1220      24.3333   -2919.3393    1043.3795   -3962.7187    1095.6802            0    760.56643    152121.29   -157940.25   -1189.6331    22748.747    233.51046    349.50414    1.0560945 
    1240    24.699158   -2942.4201    1015.5889    -3958.009    1114.7861            0    821.20595    152042.69   -157936.69   -581.49954    22545.116    227.29088     340.1868    1.0444581 
    1260     25.06694   -2965.9906    1011.5209   -3977.5115    1137.3984            0    850.69736    151972.34   -157937.95   -557.09399    22340.759    226.38045    338.85243   0.98374803 
    1280    25.506043   -2989.5484    1016.7798   -4006.3282    1160.9102            0    882.24024     151890.5   -157939.98   -93.844073    22136.859    227.55742    340.60408    1.0089629 
    1300    25.885481   -3011.5964    1043.7628   -4055.3592    1184.2311            0     891.6381    151808.85   -157940.08   -307.32007    21936.757    233.59626     349.6133    1.0504806 
    1320    26.286564   -3035.1132    1037.5333   -4072.6466     1179.597            0    903.59052    151784.33   -157940.16    -91.53774    21739.794    232.20209    347.62923    0.8833997 
    1340    26.707803   -3061.1043    1034.7198   -4095.8241    1231.5568            0    955.77666    151655.57   -157938.72    53.261099    21546.978    231.57242    346.58931    1.0307605 
    1360    27.133179    -3085.252    983.77833   -4069.0303     1230.971            0    968.86383    151669.63    -157938.5    197.66951    21360.266    220.17161    329.49241     1.002352 
    1380    27.554558   -3101.9696    1037.9918   -4139.9614    1216.6215            0    897.01691    151685.79   -157939.39   -392.64446     21180.32     232.3047    347.61632    1.0380526 
    1400    27.956349   -3124.8379     1003.328   -4128.1659    1199.4883            0    863.54306    151748.07   -157939.27   -548.32584    21003.378    224.54686    336.16828   0.85494391 
    1420    28.361482   -3146.8927    1020.9417   -4167.8344     1210.319            0    850.57584    151710.13   -157938.86   -1093.8532    20825.938    228.48885    342.04449    0.9178739 
    1440    28.768238   -3170.6554    993.33274   -4163.9882    1239.5959            0    893.87046     151642.2   -157939.65   -436.10089    20645.122    222.30991    332.79717   0.88336557 
    1460    29.177687   -3191.0873     980.2106   -4171.2979    1257.3639            0    955.42122    151554.27   -157938.35    -139.1763    20465.429    219.37314    328.30589   0.99602014 
    1480    29.586943   -3208.4185    993.92387   -4202.3424    1243.9183            0    936.28667     151555.9   -157938.45    -261.1948    20289.512     222.4422    333.01034   0.85071989 
    1500    29.995233   -3229.0775    1028.0284   -4257.1059    1272.6443            0    960.80911    151449.75   -157940.31   -307.25416    20116.744    230.07487    344.43881   0.88683413 
    1520    30.435761   -3250.8294    998.11977   -4248.9491    1282.1976            0    990.08774    151419.81   -157941.05    64.772936    19947.298    223.38125    334.38841   0.90320757 
    1540    30.853458   -3268.3168    1004.1599   -4272.4768    1299.4164            0    987.20608    151381.91   -157941.01    -80.22578    19782.738    224.73305    336.30685     1.007422 
    1560    31.279241   -3289.0826    966.08591   -4255.1685    1287.1272            0    982.95309    151416.22   -157941.47     198.4371    19622.918    216.21201    323.54353   0.99939162 
    1580    31.708028   -3306.2125    979.26815   -4285.4807    1288.5111            0    952.23769    151415.68   -157941.91   -206.26434    19467.717    219.16222     328.0518   0.90689318 
    1600    32.140092   -3325.1219    984.21128   -4309.3331     1308.258            0    963.95207    151360.81   -157942.35   -284.04656    19314.766     220.2685    329.66568    0.9610293 
    1620      32.5727   -3340.9024    1013.5306    -4354.433    1318.1025            0     944.3489    151325.17   -157942.05     -653.005    19163.698    226.83023    339.47468    1.0097397 
    1640    32.982791   -3360.2312    974.13546   -4334.3667     1312.594            0    986.63361    151308.68   -157942.28    343.78235    19013.496    218.01352    326.28924   0.99083786 
    1660    33.419277   -3375.6484    982.60503   -4358.2535    1345.3148            0    970.47388    151266.28   -157940.32   -374.81541    18867.836    219.90902    329.06869    1.0301828 
    1680    33.858902    -3394.428    981.74052   -4376.1685    1319.3919            0    955.09161    151289.81   -157940.47    -162.3498     18724.14    219.71554    328.81202   0.99514477 
    1700     34.30191   -3412.8462    973.87976   -4386.7259     1341.294            0    965.41854    151248.54   -157941.98   -351.70824    18582.062    217.95629    326.03525    1.1973975 
    1720    34.776698   -3429.9352    986.76909   -4416.7043    1362.6752            0    1013.2358    151149.58    -157942.2    37.299904    18441.349    220.84095     330.4706    1.0534043 
    1740    35.222457   -3446.5561    971.25044   -4417.8065    1381.6012            0    1046.8608    151096.61   -157942.88    336.29665    18304.289    217.36784    325.28479    1.0839935 
    1760    35.644247   -3463.1798    999.75562   -4462.9354    1395.5442            0    1012.1296    151070.28   -157940.88   -252.71902    18172.322    223.74736    334.82695    1.1205298 
    1780    36.095301   -3481.5453     991.5153   -4473.0606     1403.686            0    1029.7008    151037.13   -157943.57   -108.73918    18043.082    221.90316    332.00846    1.1669904 
    1800    36.548801   -3496.9886    965.33662   -4462.3252    1390.3088            0    1050.6761    151040.12   -157943.43    539.62368    17917.488    216.04432    323.23991    1.1447201 
    1820     37.00671    -3510.113    991.32596    -4501.439    1392.0482            0    1034.7898    151015.68   -157943.96    152.36115    17797.781    221.86078    332.04409     1.050451 
    1840    37.465953   -3528.9352    974.95032   -4503.8855    1387.6457            0    1012.5199    151036.63   -157940.68   -250.11127    17681.765    218.19588     326.4633     1.104675 
    1860    37.926741   -3545.3967    970.46573   -4515.8624    1391.3683            0    1035.1551    151000.11   -157942.49   -218.15781     17567.52    217.19222    325.05524    1.0190724 
    1880    38.391252   -3561.7398    933.83134   -4495.5711     1404.458            0    1032.7156     151010.9   -157943.64   -1.9885562    17454.833    208.99337    312.70412    1.1301542 
    1900    38.856336   -3574.6165     984.6503   -4559.2668    1422.0814            0    1060.3245    150900.79   -157942.46    190.15103     17344.24    220.36676    329.66505    1.2027369 
    1920     39.32352   -3589.0687    963.85062   -4552.9193    1427.8662            0    1075.6986    150887.22    -157943.7    506.81653    17237.394    215.71175    322.81523    1.0733524 
    1940     39.79544   -3604.8214    970.89136   -4575.7128     1416.926            0    1037.9197    150913.56   -157944.12   -60.261935    17135.412    217.28748    325.12481     1.144127 
    1960    40.270815    -3620.548    963.48434   -4584.0323    1401.1546            0    1016.5609    150941.43   -157943.17   -388.03612    17035.264    215.62977    322.67138    1.1152888 
    1980    40.749353   -3638.3971    977.90456   -4616.3017    1415.5473            0     1009.486    150904.71   -157946.04   -640.67547     16934.97    218.85705    327.48198    1.1614525 
    2000    41.229238   -3654.2588    957.08437   -4611.3432    1418.1059            0    1031.2688    150883.23   -157943.95   -595.60403    16834.098    214.19745    320.55039    1.0631632 
Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms

Pair  time (%) = 23.5391 (57.0932)
Bond  time (%) = 0.0153775 (0.0372976)
Kspce time (%) = 3.17798 (7.70806)
Neigh time (%) = 2.51543 (6.10108)
Comm  time (%) = 1.6585 (4.02262)
Outpt time (%) = 0.00876421 (0.0212572)
Other time (%) = 10.3141 (25.0165)

Nlocal:    625 ave 632 max 619 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost:    12577 ave 12644 max 12511 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:    532752 ave 581561 max 492708 min
Histogram: 1 1 0 0 0 0 1 0 0 1

Total # of neighbors = 2131009
Ave neighs/atom = 852.404
Ave special neighs/atom = 4
Neighbor list builds = 120
Dangerous builds = 16

